Related papers: Stochastic boundary conditions for molecular dynam…
We consider parabolic PDEs with randomly switching boundary conditions. In order to analyze these random PDEs, we consider more general stochastic hybrid systems and prove convergence to, and properties of, a stationary distribution.…
We present a new energy-stable open boundary condition, and an associated numerical algorithm, for simulating incompressible flows with outflow/open boundaries. This open boundary condition ensures the energy stability of the system, even…
Cellular automata can simulate many complex physical phenomena using the power of simple rules. The presented methodological platform expresses the concept of programmable matter in which Newtons laws of motion are one of examples. Energy…
Simulating the irreversible quantum dynamics of exciton and electron transfer problems poses a nontrivial challenge. Because the irreversibility of the system dynamics is a result of quantum thermal activation and dissipation caused by the…
In a stochastic reaction network setting we consider the problem of tracking the fate of individual molecules. We show that using the classical large volume limit results, we may approximate the dynamics of a single tracked molecule in a…
We investigate the use of partially twisted boundary conditions in a lattice simulation with two degenerate flavours of improved Wilson sea quarks. The use of twisted boundary conditions on a cubic volume (L^3) gives access to components of…
The developing field of stochastic thermodynamics extends concepts of macroscopic thermodynamics such as entropy production and work to the microscopic level of individual trajectories taken by a system through phase space. The scheme…
Sonoluminescence is the phenomena of light emission from a collapsing gas bubble in a liquid. Theoretical explanations of this extreme energy focusing are controversial and difficult to validate experimentally. We propose to use molecular…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
In this work a phenomenological stochastic differential equation is proposed to model the time evolution of the radius of a pre-critical molecular cluster during nucleation (the classical order parameter). Such a stochastic differential…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
Sequential Monte Carlo (SMC) algorithms represent a suite of robust computational methodologies utilized for state estimation and parameter inference within dynamical systems, particularly in real-time or online environments where data…
A binary fluid mixture in contact with lateral particle reservoirs is considered. By imposing different particle concentrations in these reservoirs, the system can be maintained under controlled non-equilibrium conditions. Previous…
This paper develops a unified methodology for probabilistic analysis and optimal control design for jump diffusion processes defined by polynomials. For such systems, the evolution of the moments of the state can be described via a system…
We introduce the stochastic Boltzmann equation (SBE) as an approach for exploring the spin dynamics of magnetic molecules coupled to a stochastic environment. The SBE is a time-evolution equation for the probability density of the spin…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Biochemical networks play a crucial role in biological systems, implementing a broad range of vital functions. They normally operate at low copy numbers and in spatial settings, but this is often ignored and well-stirred conditions are…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
Accurate representation of atmosphere-ocean boundary layers, including the interplay of turbulence, surface waves, and air-sea fluxes, remains a challenge in geophysical fluid dynamics, particularly for climate simulations. This study…